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The game plays in a similar fashion to the boss battles of Mario vs. Donkey Kong 2. The player has to aim and shoot Mini Mario toys from a rotatable cannon, which can be adjusted with the mouse by rotating the adjoined wheel and fired by clicking on the central button that reads "Shoot". The game's objective is to have at least one Mini Mario reach the exit in each of the three levels. The player starts out the game with a reserve of five Mini Marios, and the number of Mini Marios they have for the next level depends on how many of them had reached the exit in the previous level.

The layout of each level consists of multiple walls and blocks placed in a maze-like manner, with multiple paths to shoot Mini Marios onto. Only one toy can be shot at a time, and it must reach the goal before another one can be shot. Mini Marios bounce off the walls, obtaining a coin each time they bounce. The player will lose Mini Marios if they launch them into gaps or into Bob-ombs and Shy Guys, which are completely motionless. Hitting an enemy destroys both the Mini Mario and the enemy, leaving that spot clear at the cost of one Mini Mario.

The exit in the first two levels consists of a Warp Pipe, while in the third level, it is a Goal Door. For each Mini Mario that reaches the Goal Door, the player is awarded 10 coins. Regardless of whether the player wins or loses the game, the end screen always displays the final score, along with the best score achieved in previous gameplays. There is also the option to either e-mail a friend about the score, or replay the game.

A Crash Kong makes a cameo appearance on the help, transition, and game over screens. The background of every level is that of Tropical Island from Mario vs. Donkey Kong 2.